Summary of work

This notebook compares the t-SNE embeddings of the same planar Inchikeys between different instruments and instrument types. We find an unexpectedly high degree of similarity between the Velos CID and HCD platforms. The differences between other instrument types are markedly larger. The comparison between qToF and Orbitrap is inconclusive, possibly due to the high volume of data.

Note on the HTML format: because the interactive plots created with plotly inflated the notebook beyond the data limit of Github, I've converted it to a HTML file which is for some reason much smaller but preserves the interactivity of the plots.

Load libraries and functions

Load and prep data

Comparison of HCD and CID Velos instruments

Comparison of qToF and CID instrument types

Comparison of qToF and HCD instrument types

Comparison qToF and Orbitrap